Interpretive Summary: This study is the first, in dairy cattle, to compare 3 statistical methods to detect Quantitative Trait Loci (QTL). In addition to confirming the presence of several milk production QTL found in previous studies, our results indicate a highly significant QTL on BTA2 affecting protein and fat yield as well as a new QTL affecting protein percent and milk yield on BTA14. Moreover, the seemingly unusual udder conformation of daughters generated from one of the sire families in this study was exploited for QTL mapping. Our data indicate that this sire is segregating for probably only a single gene responsible for variation in udder conformation that is manifest in several udder-related conformation traits on BTA20 and additional QTL on BTA21 making these two chromosomes candidates for fine mapping to more precisely estimate the effects and locations of these QTL. Together, these results provide more genomic targets for study of causal mutations underlying economically important phenotypes. Completion of these studies will provide management tools that will enhance genetic improvement of U.S. Holsteins with respect to production and longevity.

Technical Abstract:
A genome scan was conducted in two U.S. Holstein half-sib families to identify QTL affecting milk production and conformation traits using the granddaughter design. The sires of the two studied families were related as sire and son and had 96 and 212 sons, respectively. A total of 221 microsatellite loci were scored in both families. Statistical analysis was performed using three different analytical methods; half-sib least squares regression, variance component and Bayesian infinite alleles approaches. A total of 119 sire/trait/chromosome tests were significant at the P<0.05 chromosome-wise significance level for the least squares approach. Variance component based analysis with both families analyzed jointly produced 51 trait/chromosome results with a LOD score > 1.0. Results for 22 and 37 chromosome/trait combinations were concordant between at least two of the three analytical methods for the milk production and type traits, respectively. Half-sib regression analysis yielded 13 significant results at the genome-wise level.